On Feb 18, 2011, at 2:12 PM, Ryan Golhar wrote:
It turns out the user's environment is not set up for batch jobs, only the system environment. I too added ". ~/.bashrc" to lib/galaxy/jobs/runners/drmaa.py.
I'm afraid this is a kludgy fix that will break if/when the drmaa.py file gets updated. It'll work for now, but there has got to be a better way.
I use TORQUE, but I don't use the drmaa runner. In my case I have no problems with setting the PATH in the .bashrc for the galaxy user on my cluster. Is there a particular reason why you want to use the drmaa runner instead of the PBS runner if your cluster uses TORQUE?
On 2/18/11 1:30 PM, Zhibin Lu wrote:
Hi,
I had same problem since we do not install software in the system directory. I had to add PATH into ./lib/galaxy/jobs/runners/drmaa.py manually. I do not know if anyone has better solution.
Zhibin Lu Bioinformatics Support
Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3
www.oicr.on.ca
Date: Fri, 18 Feb 2011 13:17:26 -0500 From: nate@bx.psu.edu To: golharam@umdnj.edu CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cluster path question
Ryan Golhar wrote:
Ryan Golhar wrote:
I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque however the jobs keep failing, because the tools are in the default system path.
How do I tell galaxy to append a directory to the path used by jobs?
Hi Ryan,
Whatever user is running the jobs will need to modify the $PATH in its shell startup files. If you're using bash, this would probably be ~/.bash_profile
It already is in .bashrc (which is called by .bash_profile) for the galaxy user. I can submit the script from the shell and it runs okay so something is up with either how the galaxy app is submitting the job or the environment being used by the galaxy job.
When you say submit via the shell, do you mean with qsub, or by logging in to a node and running the wrapper script?
I haven't tested Torque with the drmaa runner so perhaps it's submitting in a way which starts the shell in non-interactive, non-login mode. Let me know if you can determine for certain that no shell startup files are being read, and I'll try to replicate this in my environment.
I'd like to modify the job script to print out some debugging information to determine what environment variables are set when the job gets executed. Actually, this would be a useful "tool" within Galaxy to test the cluster.
That's probably the simplest method, to just create a tool that outputs (either to stdout or the output file) what you'd like to see.
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